Automatic compilation of MATLAB programs for synergistic execution on heterogeneous processors

MATLAB is an array language, initially popular for rapid prototyping, but is now being increasingly used to develop production code for numerical and scientific applications. Typical MATLAB programs have abundant data parallelism. These programs also have control flow dominated scalar regions that have an impact on the program's execution time. Today's computer systems have tremendous computing power in the form of traditional CPU cores and throughput oriented accelerators such as graphics processing units(GPUs). Thus, an approach that maps the control flow dominated regions to the CPU and the data parallel regions to the GPU can significantly improve program performance. In this paper, we present the design and implementation of MEGHA, a compiler that automatically compiles MATLAB programs to enable synergistic execution on heterogeneous processors. Our solution is fully automated and does not require programmer input for identifying data parallel regions. We propose a set of compiler optimizations tailored for MATLAB. Our compiler identifies data parallel regions of the program and composes them into kernels. The problem of combining statements into kernels is formulated as a constrained graph clustering problem. Heuristics are presented to map identified kernels to either the CPU or GPU so that kernel execution on the CPU and the GPU happens synergistically and the amount of data transfer needed is minimized. In order to ensure required data movement for dependencies across basic blocks, we propose a data flow analysis and edge splitting strategy. Thus our compiler automatically handles composition of kernels, mapping of kernels to CPU and GPU, scheduling and insertion of required data transfer. The proposed compiler was implemented and experimental evaluation using a set of MATLAB benchmarks shows that our approach achieves a geometric mean speedup of 19.8X for data parallel benchmarks over native execution of MATLAB.

Exploration of deleterious single nucleotide polymorphisms in the components of human P bodies: An in silico approach

P bodies are 100-300 nm sized organelles involved in mRNA silencing and degradation. A total of 60 human proteins have been reported to localize to P bodies. Several human SNPs contribute to complex diseases by altering the structure and function of the proteins. Also, SNPs alter various transcription factors binding, splicing and miRNA regulatory sites. Owing to the essential functions of P bodies in mRNA regulation, we explored computationally the functional significance of SNPs in 7 P body components such as XRN1, DCP2, EDC3, CPEB1, GEMIN5, STAU1 and TRIM71. Computational analyses of non-synonymous SNPs of these components was initiated using well utilized publicly available software programs such as the SIFT, followed by PolyPhen, PANTHER, MutPred, I-Mutant-2.0 and PhosSNP 1.0. Functional significance of noncoding SNPs in the regulatory regions were analysed using FastSNP. Utilizing miRSNP database, we explored the role of SNPs in the context that alters the miRNA binding sites in the above mentioned genes. Our in silico studies have identified various deleterious SNPs and this cataloguing is essential and gives first hand information for further analysis by in vitro and in vivo methods for a better understanding of maintenance, assembly and functional aspects of P bodies in both health and disease. (C) 2013 Elsevier B.V. All rights reserved.

TCP: thread contention predictor for parallel programs

With proliferation of chip multicores (CMPs) on desktops and embedded platforms, multi-threaded programs have become ubiquitous. Existence of multiple threads may cause resource contention, such as, in on-chip shared cache and interconnects, depending upon how they access resources. Hence, we propose a tool - Thread Contention Predictor (TCP) to help quantify the number of threads sharing data and their sharing pattern. We demonstrate its use to predict a more profitable shared, last level on-chip cache (LLC) access policy on CMPs. Our cache configuration predictor is 2.2 times faster compared to the cycle-accurate simulations. We also demonstrate its use for identifying hot data structures in a program which may cause performance degradation due to false data sharing. We fix layout of such data structures and show up-to 10% and 18% improvement in execution time and energy-delay product (EDP), respectively.

Static analysis for checking data format compatibility of programs

Large software systems are developed by composing multiple programs. If the programs manip-ulate and exchange complex data, such as network packets or files, it is essential to establish that they follow compatible data formats. Most of the complexity of data formats is associated with the headers. In this paper, we address compatibility of programs operating over headers of network packets, files, images, etc. As format specifications are rarely available, we infer the format associated with headers by a program as a set of guarded layouts. In terms of these formats, we define and check compatibility of (a) producer-consumer programs and (b) different versions of producer (or consumer) programs. A compatible producer-consumer pair is free of type mismatches and logical incompatibilities such as the consumer rejecting valid outputs gen-erated by the producer. A backward compatible producer (resp. consumer) is guaranteed to be compatible with consumers (resp. producers) that were compatible with its older version. With our prototype tool, we identified 5 known bugs and 1 potential bug in (a) sender-receiver modules of Linux network drivers of 3 vendors and (b) different versions of a TIFF image library.

Triarylborane-dipyrromethane conjugates bearing dual receptor sites: the synthesis and evaluation of the anion binding site preference

The synthesis and optical properties of four new triarylborane-dipyrromethane (TAB-DPM) conjugates (3a-d) containing dual binding sites (hydrogen bond donor and Lewis acid) have been reported. The new compounds exhibit a selective fluorogenic response towards the F-ion. The NMR titrations show that the anions bind to the TAB-DPM conjugates via the Lewis acidic triarylborane centre in preference to the hydrogen bond donor (dipyrromethane) units.

PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites

Knowledge of protein-ligand interactions is essential to understand several biological processes and important for applications ranging from understanding protein function to drug discovery and protein engineering. Here, we describe an algorithm for the comparison of three-dimensional ligand-binding sites in protein structures. A previously described algorithm, PocketMatch (version 1.0) is optimised, expanded, and MPI-enabled for parallel execution. PocketMatch (version 2.0) rapidly quantifies binding-site similarity based on structural descriptors such as residue nature and interatomic distances. Atomic-scale alignments may also be obtained from amino acid residue pairings generated. It allows an end-user to compute database-wide, all-to-all comparisons in a matter of hours. The use of our algorithm on a sample dataset, performance-analysis, and annotated source code is also included.

Colorimetric anion sensor based on receptor having indole- and thiourea-binding sites

A new colorimetric sensor L containing nitro-substituted indole and bisthiocarbonohydrazone units for selective fluoride and acetate ions is designed and synthesized. The receptor L shows well-defined color change in the visible region of the spectrum with an absorption band at similar to 515 nm and 506 nm, respectively, for the F- and CH3COO- ions in an acetonitrile solution. Job's plots indicated the formation of 1 : 1 (L with CH3COO-) and 1 : 2 (L with F-) complexes. The interaction of L with the F- ion undergoes a deprotonation process and release of HX2](-), whereas with the CH3COO- ion, it forms a stable LH2(...)X](-) complex. The relative affinities of the anions with L are rationalized using computational studies.

Context dependency of rewards and services in an Indian ant-plant interaction: southern sites favour the mutualism between plants and ants

Protection-based ant-plant mutualisms may vary in strength due to differences in ant rewards, abundance of protective ants and herbivory pressure. We investigated geographical and temporal variation in host plant traits and herbivory pressure at five sites spanning the distribution range of the myrmecophyte Humboldtia brunonis (Fabaceae) in the Indian Western Ghats. Southern siteshad, onaverage, 2.4 times greater abundance of domatia-bearing individuals, 1.6 times greater extrafloral nectary numbers per leaf, 1.2 times larger extrafloral nectary sizes, 2.2 times greater extrafloral nectar (EFN) volumes and a two-fold increase in total amino acid and total sugar concentrations in EFN compared with northern sites. Astrong protection-based mutualismwith ants occurred at only one southern site where herbivory was highest, suggesting that investments in attracting ants correlate with anti-herbivore benefits gained from the presence of protective ants. Our results confirm a temporally stable north-south gradient in myrmecophytic traits in this ant-plant as several of these traits were re-sampled after a 5-y interval. However, the chemical composition of EFN varied at both spatial and short-term temporal scales suggesting that only repeated measurements of rewards such as EFN can reveal the real spectrum of trait variation in an ant-plant mutualistic system.

Genomic mapping of cAMP receptor protein (CRPMt) in Mycobacterium tuberculosis: relation to transcriptional start sites and the role of CRPMt as a transcription factor

Chromatin immunoprecipitation identified 191 binding sites of Mycobacterium tuberculosis cAMP receptor protein (CRPMt) at endogenous expression levels using a specific alpha-CRPMt antibody. Under these native conditions an equal distribution between intragenic and intergenic locations was observed. CRPMt binding overlapped a palindromic consensus sequence. Analysis by RNA sequencing revealed widespread changes in transcriptional profile in a mutant strain lacking CRPMt during exponential growth, and in response to nutrient starvation. Differential expression of genes with a CRPMt-binding site represented only a minor portion of this transcriptional reprogramming with similar to 19% of those representing transcriptional regulators potentially controlled by CRPMt. The subset of genes that are differentially expressed in the deletion mutant under both culture conditions conformed to a pattern resembling canonical CRP regulation in Escherichia coli, with binding close to the transcriptional start site associated with repression and upstream binding with activation. CRPMt can function as a classical transcription factor in M. tuberculosis, though this occurs at only a subset of CRPMt-binding sites.

Precise Slicing in Imperative Programs via Term-Rewriting and Abstract Interpretation

We propose a new approach for producing precise constrained slices of programs in a language such as C. We build upon a previous approach for this problem, which is based on term-rewriting, which primarily targets loop-free fragments and is fully precise in this setting. We incorporate abstract interpretation into term-rewriting, using a given arbitrary abstract lattice, resulting in a novel technique for slicing loops whose precision is linked to the power of the given abstract lattice. We address pointers in a first-class manner, including when they are used within loops to traverse and update recursive data structures. Finally, we illustrate the comparative precision of our slices over those of previous approaches using representative examples.

Simultaneous co-ordination of three cytosine ligands displaying different binding sites around the copper centres

We report the synthesis and structural characterization of a polymeric ternary copper-cytosine-phenanthroline complex, Cu-4(phen)(3)-(mu(3)-cyt)(2)(mu-OH)(cyt)(OH)Cl-3](n)center dot 16H(2)O, where three cytosine ligands with different binding sites have simultaneously complexed to the four copper metal centres. Interestingly, the complex exhibits two different coordination geometries around the metal centres.

Synthesis and crystal structure of copper (II) uracil ternary polymeric complex with 1,10-phenanthroline along with the Hirshfeld surface analysis of the metal binding sites for the uracil ligand

The study of models for ``metal-enzyme-substrate'' interaction has been a proactive area of research owing to its biological and pharmacological importance. In this regard the ternary copper uracil complex with 1,10-phenanthroline represents metal-enzyme-substrate system for DNA binding enzymes. The synthesis of the complex, followed by slow evaporation of the reaction mixture forms two concomitant solvatomorph crystals viz., {Cu(phen)(mu-ura)(H2O)](n)center dot H2O (1a)} and {Cu(phen)(mu-ura)(H2O)](n)center dot CH3OH (1b)}. Both complexes are structurally characterized, while elemental analysis, IR and EPR spectra were recorded for 1b (major product). In both complexes, uracil coordinates uniquely via N1 and N3 nitrogen atom acting as a bidentate bridging ligand forming a 1-D polymer. The two solvatomorphs were quantitatively analyzed for the differences with the aid of Hirshfeld surface analysis. (C) 2014 Elsevier B.V. All rights reserved.

Compiler/Runtime Framework for Dynamic Dataflow Parallelization of Tiled Programs

Task-parallel languages are increasingly popular. Many of them provide expressive mechanisms for intertask synchronization. For example, OpenMP 4.0 will integrate data-driven execution semantics derived from the StarSs research language. Compared to the more restrictive data-parallel and fork-join concurrency models, the advanced features being introduced into task-parallelmodels in turn enable improved scalability through load balancing, memory latency hiding, mitigation of the pressure on memory bandwidth, and, as a side effect, reduced power consumption. In this article, we develop a systematic approach to compile loop nests into concurrent, dynamically constructed graphs of dependent tasks. We propose a simple and effective heuristic that selects the most profitable parallelization idiom for every dependence type and communication pattern. This heuristic enables the extraction of interband parallelism (cross-barrier parallelism) in a number of numerical computations that range from linear algebra to structured grids and image processing. The proposed static analysis and code generation alleviates the burden of a full-blown dependence resolver to track the readiness of tasks at runtime. We evaluate our approach and algorithms in the PPCG compiler, targeting OpenStream, a representative dataflow task-parallel language with explicit intertask dependences and a lightweight runtime. Experimental results demonstrate the effectiveness of the approach.

Evaluating Methods to Predict Streamflow at Ungauged Sites using Regional Flow Duration Curves: A Case Study

Precise information on streamflows is of major importance for planning and monitoring of water resources schemes related to hydro power, water supply, irrigation, flood control, and for maintaining ecosystem. Engineers encounter challenges when streamflow data are either unavailable or inadequate at target locations. To address these challenges, there have been efforts to develop methodologies that facilitate prediction of streamflow at ungauged sites. Conventionally, time intensive and data exhaustive rainfall-runoff models are used to arrive at streamflow at ungauged sites. Most recent studies show improved methods based on regionalization using Flow Duration Curves (FDCs). A FDC is a graphical representation of streamflow variability, which is a plot between streamflow values and their corresponding exceedance probabilities that are determined using a plotting position formula. It provides information on the percentage of time any specified magnitude of streamflow is equaled or exceeded. The present study assesses the effectiveness of two methods to predict streamflow at ungauged sites by application to catchments in Mahanadi river basin, India. The methods considered are (i) Regional flow duration curve method, and (ii) Area Ratio method. The first method involves (a) the development of regression relationships between percentile flows and attributes of catchments in the study area, (b) use of the relationships to construct regional FDC for the ungauged site, and (c) use of a spatial interpolation technique to decode information in FDC to construct streamflow time series for the ungauged site. Area ratio method is conventionally used to transfer streamflow related information from gauged sites to ungauged sites. Attributes that have been considered for the analysis include variables representing hydrology, climatology, topography, land-use/land- cover and soil properties corresponding to catchments in the study area. Effectiveness of the presented methods is assessed using jack knife cross-validation. Conclusions based on the study are presented and discussed. (C) 2015 The Authors. Published by Elsevier B.V.

A Pd-24 Pregnant Molecular Nanoball: Self-Templated Stellation by Precise Mapping of Coordination Sites

We found that Pd(II) ion (M) and the smallest 120 bidentate donor pyrimidine (L-a) self-assemble into a mononuclear M(L-a)(4) complex (1a) instead of the expected smallest M-12(L-a)(24) molecular ball (1), presumably due to the weak coordination nature of the pyrimidine. To construct such a pyrimidine bridged nanoball, we employed a new donor tris(4-(pyrimidin-5-yl)phenyl)amine (L); which upon selective complexation with Pd(II) ions resulted in the formation of a pregnant M24L24 molecular nanoball (2) consisting of a pyrimidine-bridged Pd-12 baby-ball supported by a Pd-12 larger mother-ball. The formation of the baby-ball was not successful without the support of the mother-ball. Thus, we created an example of a self-assembly where the inner baby-ball resembling to the predicted M-12(L-a)(24) ball (1) was incarcerated by the giant outer mother-ball by means of geometrical constraints. Facile conversion of the pregnant ball 2 to a smaller M-12(L-b)(24) ball 3 with dipyridyl donor was achieved in a single step.